Empathy is a crucial aspect of our daily lives, as it enhances our wellbeing and is a proxy for prosocial behavior. It encompasses two related but partially distinct components: cognitive and affective empathy. Both are susceptible to context, biases and an individual’s physiological state. Few studies have explored the effects of a person’s mood on these empathy components, and results are mixed. The current study takes advantage of an ecological, naturalistic empathy task – the empathic accuracy (EA) task – in combination with physiological measurements to examine and differentiate between the effects of one’s mood on both empathy components. Participants were induced with positive or negative mood and presented videos of targets narrating autobiographical negative stories, selected from a Chinese empathy dataset that we developed (now publicly available). The stories were conveyed in audio-only, visual-only and full-video formats. Participants rated the target’s emotional state while watching or listening to their stories, and physiological measures were taken throughout the process. Importantly, similar measures were taken from the targets when they narrated the stories, allowing a comparison between participants’ and targets’ measures. We found that in audio-only and visual-only conditions, participants whose moods were congruent with the target showed higher physiological synchrony than those with incongruent mood, implying a mood-congruency effect on affective empathy. However, there was no mood effect on empathic accuracy (reflecting cognitive empathy), suggesting a different influence of mood on the two empathy components.